Msx1 (msh homeobox 1) - Rat Genome Database
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Gene: Msx1 (msh homeobox 1) Rattus norvegicus
Analyze
Symbol: Msx1
Name: msh homeobox 1
RGD ID: 620929
Description: Predicted to have DNA-binding transcription factor activity, RNA polymerase II-specific; p53 binding activity; and transcription regulatory region sequence-specific DNA binding activity. Involved in cartilage development; cellular response to nicotine; and pituitary gland development. Predicted to localize to nucleoplasm and transcription regulator complex. Biomarker of cryptorchidism. Human ortholog(s) of this gene implicated in cleft lip; cleft palate; orofacial cleft 5; tooth and nail syndrome; and tooth disease (multiple). Orthologous to human MSX1 (msh homeobox 1); INTERACTS WITH (S)-nicotine; 1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: homeo box, msh-like 1; homeobox protein MSX-1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
NCBI Annotation Information: Annotation category: partial on reference assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21472,961,170 - 72,964,970 (+)NCBI
Rnor_6.0 Ensembl1477,712,240 - 77,716,059 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01477,712,262 - 77,716,061 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01477,690,990 - 77,694,789 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41478,257,345 - 78,261,144 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11478,259,735 - 78,263,533 (+)NCBI
Celera1471,923,586 - 71,927,385 (+)NCBICelera
Cytogenetic Map14q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of meiosis  (ISO)
anterior/posterior pattern specification  (ISO)
BMP signaling pathway  (ISO)
BMP signaling pathway involved in heart development  (ISO)
bone morphogenesis  (ISO)
cartilage development  (IMP)
cartilage morphogenesis  (ISO)
cell morphogenesis  (ISO)
cellular response to nicotine  (IEP)
embryonic digit morphogenesis  (ISO)
embryonic forelimb morphogenesis  (ISO)
embryonic hindlimb morphogenesis  (ISO)
embryonic limb morphogenesis  (ISO)
embryonic morphogenesis  (IBA)
embryonic nail plate morphogenesis  (ISO)
epithelial to mesenchymal transition  (ISO)
epithelial to mesenchymal transition involved in endocardial cushion formation  (ISO)
face morphogenesis  (ISO)
forebrain development  (ISO)
heart development  (ISO)
heart morphogenesis  (ISO)
in utero embryonic development  (ISO)
mammary gland epithelium development  (ISO)
mesenchymal cell proliferation  (ISO)
midbrain development  (ISO)
middle ear morphogenesis  (ISO)
muscle organ development  (ISO)
negative regulation of apoptotic process  (ISO)
negative regulation of cell growth  (ISO)
negative regulation of cell population proliferation  (ISO)
negative regulation of DNA binding  (ISO)
negative regulation of striated muscle cell differentiation  (ISO)
negative regulation of transcription by RNA polymerase II  (ISO)
negative regulation of transcription regulatory region DNA binding  (ISO)
negative regulation of transcription, DNA-templated  (ISO)
odontogenesis  (ISO)
odontogenesis of dentin-containing tooth  (ISO)
pituitary gland development  (IEP)
positive regulation of BMP signaling pathway  (ISO)
positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator  (ISO)
positive regulation of mesenchymal cell apoptotic process  (ISO)
positive regulation of transcription by RNA polymerase II  (ISO)
protein localization to nucleus  (ISO)
protein stabilization  (ISO)
regulation of odontogenesis  (ISO)
regulation of transcription by RNA polymerase II  (IBA)
roof of mouth development  (ISO)
signal transduction involved in regulation of gene expression  (ISO)
stem cell differentiation  (ISO)

Cellular Component

References

Additional References at PubMed
PMID:7916326   PMID:8858134   PMID:8861098   PMID:8898217   PMID:9369446   PMID:9697309   PMID:10340755   PMID:10742093   PMID:10742104   PMID:11023873   PMID:11332647   PMID:11369996  
PMID:12489152   PMID:12651933   PMID:15188430   PMID:15192231   PMID:15217086   PMID:15705871   PMID:15930102   PMID:16002402   PMID:16330189   PMID:17030628   PMID:17601530   PMID:17693062  
PMID:18285513   PMID:18590716   PMID:18667074   PMID:19422820   PMID:20004191   PMID:20123092   PMID:21465616   PMID:22071108   PMID:27741242  


Genomics

Comparative Map Data
Msx1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21472,961,170 - 72,964,970 (+)NCBI
Rnor_6.0 Ensembl1477,712,240 - 77,716,059 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01477,712,262 - 77,716,061 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01477,690,990 - 77,694,789 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41478,257,345 - 78,261,144 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11478,259,735 - 78,263,533 (+)NCBI
Celera1471,923,586 - 71,927,385 (+)NCBICelera
Cytogenetic Map14q21NCBI
MSX1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl44,859,665 - 4,863,936 (+)EnsemblGRCh38hg38GRCh38
GRCh3844,859,665 - 4,863,936 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3744,861,392 - 4,865,663 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3644,912,293 - 4,916,564 (+)NCBINCBI36hg18NCBI36
Build 3444,979,477 - 4,983,530NCBI
Celera44,758,413 - 4,762,671 (+)NCBI
Cytogenetic Map4p16.2NCBI
HuRef44,797,648 - 4,801,917 (+)NCBIHuRef
CHM1_144,859,330 - 4,863,591 (+)NCBICHM1_1
Msx1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39537,977,835 - 37,981,929 (-)NCBIGRCm39mm39
GRCm38537,820,491 - 37,824,585 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl537,820,485 - 37,824,583 (-)EnsemblGRCm38mm10GRCm38
MGSCv37538,211,730 - 38,215,824 (-)NCBIGRCm37mm9NCBIm37
MGSCv36538,108,742 - 38,112,705 (-)NCBImm8
Celera535,276,257 - 35,280,351 (-)NCBICelera
Cytogenetic Map5B3NCBI
cM Map520.21NCBI
Msx1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555144,923,552 - 4,927,471 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555144,923,552 - 4,927,471 (-)NCBIChiLan1.0ChiLan1.0
MSX1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.144,935,603 - 4,939,117 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl44,935,600 - 4,939,079 (+)Ensemblpanpan1.1panPan2
MSX1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl370,232,052 - 70,236,447 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1370,232,790 - 70,236,295 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Msx1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493647717,406,551 - 17,413,615 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MSX1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl85,628,377 - 5,632,608 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.185,628,381 - 5,632,375 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.285,246,698 - 5,250,692 (-)NCBISscrofa10.2Sscrofa10.2susScr3
MSX1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12741,028,763 - 41,032,676 (+)NCBI
ChlSab1.1 Ensembl2741,028,919 - 41,033,006 (+)Ensembl
Msx1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475521,857,360 - 21,861,235 (+)NCBI

Position Markers
RH130342  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01477,715,700 - 77,715,883NCBIRnor6.0
Rnor_5.01477,694,428 - 77,694,611UniSTSRnor5.0
RGSC_v3.41478,260,783 - 78,260,966UniSTSRGSC3.4
Celera1471,927,024 - 71,927,207UniSTS
Cytogenetic Map14q21UniSTS
AI324650  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01477,715,774 - 77,715,890NCBIRnor6.0
Rnor_5.01477,694,502 - 77,694,618UniSTSRnor5.0
RGSC_v3.41478,260,857 - 78,260,973UniSTSRGSC3.4
Celera1471,927,098 - 71,927,214UniSTS
Cytogenetic Map14q21UniSTS
Msx1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01477,712,356 - 77,712,815NCBIRnor6.0
Rnor_5.01477,691,084 - 77,691,543UniSTSRnor5.0
Celera1471,923,680 - 71,924,139UniSTS
Cytogenetic Map14q21UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1412680424106641756Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143259392686191589Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)144031561085315610Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)144031561085315610Rat
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)144031561085315610Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)144031561085315610Rat
70214Niddm28Non-insulin dependent diabetes mellitus QTL 284.06blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)144163756980841518Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1442442731108833671Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1443910761105074364Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1451818462105074364Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1460980905105980905Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1460980905105980905Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)146187332388870994Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1461993178106993178Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1463548095108548095Rat
70153Bp59Blood pressure QTL 593.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)147339146788870994Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:384
Count of miRNA genes:212
Interacting mature miRNAs:248
Transcripts:ENSRNOT00000009101
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 23 9
Low 41 9 4 9 4 8 11 51 23 24 11 8
Below cutoff 3 33 22 10 22 12 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009101   ⟹   ENSRNOP00000009101
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1477,712,240 - 77,716,059 (+)Ensembl
RefSeq Acc Id: NM_031059   ⟹   NP_112321
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21472,961,170 - 72,964,970 (+)NCBI
Rnor_6.01477,712,262 - 77,716,061 (+)NCBI
Rnor_5.01477,690,990 - 77,694,789 (+)NCBI
RGSC_v3.41478,257,345 - 78,261,144 (+)RGD
Celera1471,923,586 - 71,927,385 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_112321 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAK70504 (Get FASTA)   NCBI Sequence Viewer  
  BAA11750 (Get FASTA)   NCBI Sequence Viewer  
  EDM00020 (Get FASTA)   NCBI Sequence Viewer  
  EDM00021 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_112321   ⟸   NM_031059
- UniProtKB: Q9QUG0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000009101   ⟸   ENSRNOT00000009101
Protein Domains
Homeobox

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620929 AgrOrtholog
Ensembl Genes ENSRNOG00000006876 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000009101 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009101 ENTREZGENE, UniProtKB/TrEMBL
InterPro Homeobox UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeobox_metazoa UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
KEGG Report rno:81710 UniProtKB/TrEMBL
NCBI Gene 81710 ENTREZGENE
Pfam Homeobox UniProtKB/TrEMBL
PhenoGen Msx1 PhenoGen
PRINTS HOMEOBOX UniProtKB/TrEMBL
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt G3V6U7_RAT UniProtKB/TrEMBL
  Q9QUG0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-09 Msx1  msh homeobox 1  Msx1  homeo box, msh-like 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-02-26 Msx1  homeo box, msh-like 1      Symbol and Name status set to approved 625702 APPROVED
2002-08-07 Msx1  homeo box, msh-like 1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in dental and craniofacial tissues 724434